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BEAST 2: a software platform for Bayesian evolutionary analysis
Remco Bouckaert1, Joseph Heled1, Denise Kühnert2
1Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand.
Plos Computational Biology
|April 12, 2014
Summary
BEAST 2 is a new, flexible Bayesian evolutionary analysis platform. It features a package manager for easy extensibility and improved MCMC chain management for complex analyses.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Bioinformatics
Background:
- BEAST 1, a popular platform for Bayesian evolutionary analysis, had structural deficiencies.
- Lack of post-deployment extensibility limited its adaptability and feature integration.
Purpose of the Study:
- Introduce BEAST 2, an open-source, extensible, and flexible software platform for Bayesian evolutionary analysis.
- Address the limitations of BEAST 1 through a redesigned architecture and enhanced features.
Main Methods:
- Developed a new software platform, BEAST 2, with a redesigned architecture.
- Implemented a package management system for third-party extensions.
- Integrated MCMC chain state read/write functionality for checkpointing and distributed computing.
- Enhanced user interface integration using XML templates for seamless functionality addition.
Main Results:
- BEAST 2 offers enhanced extensibility through its package management system.
- New models for birth-death-sampling tree priors, phylodynamics, and model averaging are readily integrated.
- Improved MCMC chain management facilitates checkpointing and high-performance computing.
- Seamless integration between the analysis engine and user interface (BEAUti 2) simplifies workflow.
Conclusions:
- BEAST 2 provides a significantly more flexible and extensible platform for Bayesian evolutionary analysis.
- The new architecture and features support advanced analyses and facilitate easier development of new functionalities.
- BEAST 2 is poised to advance research in phylogenetics, phylodynamics, and evolutionary modeling.
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